In the beef and dairy industries, horns on cattle are the cause of several economic and management problems. Horns pose hazards to animal handlers and also to other cattle causing large economic losses due to bruising. Difficulty in calving (dystocia) has been associated with horns and the widespread practice of dehorning young cattle has been shown to be stressful and reduce growth rates (Goonewardene et al., (1999) Can. J. Anim. Sci. 79:383-385).
Polled (hornless) cattle are found in modern breeds and evidence of polled cattle dates back to the Miocene epoch, well before the domestication of cattle. In some breeds (e.g. Angus) the polled condition has been selected for but in others such as Hereford, the breed was established with the horned phenotype. There is increasing pressure from the live export and feedlot trades on producers to sell hornless cattle. Selective breeding with polled cattle is the means of introgressing the polled trait into horned cattle breeds.
A single gene in cattle controls the horn development trait and the polled phenotype is dominant to the horned phenotype. Thus, hornless cattle may be either heterozygous (horned carriers) or homozygous for the polled allele and the ability to distinguish between carriers and non-carriers is crucial to breeding programs. The physical detection of horned or polled cattle is further complicated by the presence of scurs. Scurs are rudimentary horns that are usually small and loosely attached to the head but can be large and attached well enough to make them difficult to distinguish from horns (Brenneman et al. (1996) J Hered 87:156-161), particularly by the untrained. The scur locus maps to bovine chromosome 19 and is thought to be expressed only in conjunction with the heterozygous horned/polled genotype and masked by the homozygous polled condition (Asai-Coakwell (2002) International Society for Animal Genetics; Schmutz et al., (1995) Mamm Genome 6:710-713). Horn growth makes it impossible for scurs to develop at the same spot, but the horned animals can still carry the gene for scurs. Scurs typically do not appear until about 4 months of age and, if left on, stop growing at a few inches. It can sometimes be difficult to distinguish horns from scurs in a young animal. However, the condition (scurs vs horns) can be easily recognized in a mature animal by one skilled in the art. Nevertheless, a definitive genetic test would greatly facilitate the breeding of polled cattle by obviating the need to distinguish scurs from horns at any stage of animal development.
The polled locus has been mapped to the centromeric region of bovine chromosome 1 (BTA1) (Georges et al. (1993) Nature Genet 4:206-210) but the gene has not been identified. The discovery of genetic markers very closely linked to the polled gene would allow the use of marker-assisted selection (MAS) as a breeding tool. Several groups have conducted linkage studies using families segregating for the horned and polled phenotypes with DNA markers (mostly microsatellites). The gene is located near the centromere of BTA1 (Harlizius et al. (1997) Mamm Genome 8:255-257). Linkage was found for several markers but the data were insufficient to order the genes within the markers.
There is currently no commercial genetic test available in the U.S. to distinguish horned and polled alleles. A test is available at Bova-Can laboratories in Canada that uses 4 microsatellite markers but this test requires samples from complete informative families. Along with the sample from the polled animal being tested, they request samples from a horned full-sib and both polled parents. It is recommended that an extended pedigree is provided before it can be determined if the test will be possible.
DNA analysis provides a powerful tool for distinguish horned and polled alleles of individual animals. Single nucleotide polymorphisms (SNP) are likely to become the standard marker for such identification because of the ease of scoring, low cost assay development and high-throughput capability. Compared with other types of DNA markers, single nucleotide polymorphisms (SNPs) are attractive because they are abundant, genetically stable, and amenable to high-throughput automated analysis. In cattle, the challenge has been to identify a minimal set of SNPs with sufficient power for use in a variety of popular breeds and crossbred populations. SNPs are DNA sequence variations that occur when a single nucleotide in the animal mt-DNA or nuclear genome sequence is altered and detected by traditionally direct DNA sequencing protocol. For example, a SNP might change the DNA sequence AAGGCTAA to ATGGCTAA. SNPs occur at one SNP every 1.9 kilobases in the human genome. SNPs can occur in both coding (gene) and noncoding regions of the genome. Many SNPs have no effect on cell function, but it is believed that others could predispose organism to disease or influence their response to a challenge. SNPs are evolutionarily stable—not changing much from generation to generation—making them easier to follow in population studies. SNPs also have properties that make them particularly attractive for genetic studies. They are more frequent than microsatellite markers, providing markers near to or in the locus of interest, some located within the gene (cSNP), which can directly influence protein structure or expression levels, giving insights into functional mechanisms.
Accordingly, there remains a need for methods and compositions that provide information regarding SNP markers that can distinguish between the bovine horned and polled alleles and thus heterozygous and homozygous polled animals.